Bill,
   Looking through the changes in the abps_tools.py script from
pymol 1.r1 to the current 1.2r2, I believe I've found the offending
code. If I revert the change...

--- modules/pmg_tk/startup/apbs_tools.py.broken 2009-12-04 11:11:03.000000000 
-0500
+++ modules/pmg_tk/startup/apbs_tools.py        2009-12-04 11:18:08.000000000 
-0500
@@ -1124,7 +1124,7 @@
         self.showAppModal()
          
     def showAppModal(self):
-        self.dialog.activate(geometry = 'centerscreenfirst', globalMode = 
'nograb')
+        #self.dialog.activate(geometry = 'centerscreenfirst', globalMode = 
'nograb')
         self.dialog.show()
         #self.dialog.activate(geometry = 'centerscreenalways')
 
I find that the use of the ABPS tools window no longer nukes the use of the 
main tk
interface menus afterwards. You may want to update the current pymol-py package 
with
that change. I haven't tested it yet but this might also solve the same issue 
with
pymol-py and the current x86_64 blt package.
                   Jack

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